I am installing a package (called CLASS, widely used in cosmology) which cannot be compiled with Apple's gcc.
I tried installing gcc by homebrew (gcc-9) and anaconda separately. But both of them could not find the standard C-library files such as stdio.h, math.h etc. I saw this problem very common in mac. I found the standard C-library files at /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/. Focusing on anaconda gcc (version 4.8.5), I then copied the files to /Users/satadru/anaconda2/include/. Now simple C-codes, such as a 'hello world' code runs fine. But when I tried to install the CLASS package, I get error arising from the problematic library files: stdio.h, math.h!! I get same error when I try to install the package using homebrew gcc-9 (after copying the library files to its concerned directory). I know that many people could run the package on catalina without any issue.
Now I have the following questions:
Are all standard C-library header files same? In other words, be it anaconda gcc 4.8.5, or gcc-9, the header files are same? Do the header files vary on different os, say linux or mac os?
Does anaconda gcc look for the header files at /Users/satadru/anaconda2/include/?
Before copying all the header files to /Users/satadru/anaconda2/include/, the directory had a few present there.
Why does not anaconda gcc installation place all of its own header files in this directory at the time of installation? Is it same when we do it on linux os?
How to solve my problem? I contacted the owner of the package and he says he himself runs the code on mac os catalina, but never faced this issue.
More information:
xcode-select --install
gives
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
which gcc gives /Users/satadru/anaconda2/bin/gcc
gcc -v gives
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Users/satadru/anaconda2/bin/../libexec/gcc/x86_64-apple-darwin11.4.2/4.8.5/lto-wrapper
Target: x86_64-apple-darwin11.4.2
Configured with: ./configure --prefix=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac --with-gxx-include-dir=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/gcc/include/c++ --bindir=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin --datarootdir=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/share --libdir=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib --with-gmp=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac --with-mpfr=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac --with-mpc=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac --with-isl=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac --with-cloog=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac --with-boot-ldflags='-Wl,-headerpad_max_install_names -Wl,-L/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-L/usr/lib' --with-stage1-ldflags='-Wl,-headerpad_max_install_names -Wl,-L/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-L/usr/lib' --enable-checking=release --with-tune=generic --disable-multilib
Thread model: posix
gcc version 4.8.5 (GCC)
Related
I am trying to use address sanitization when calling my program with clang, however it doesn't seem to be installed. If I type which llvm-symbolizer I get llvm-symbolizer not found. I also checked under /usr/bin and /usr/local/bin and under the location where clang is installed /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin but still I can't find llvm-symbolizer (though there are other llvm-* executables in the last path).
Is there a way I can install this on macos? Also, I couldn't find it in brew. I am using clang built in macos: Apple clang version 12.0.0 (clang-1200.0.32.21).
My version of llvm-symbolizer was installed with Homebrew. You have to install llvm with brew install llvm to get it. It then shows up as:
% which llvm-symbolizer
/usr/local/Cellar/llvm/11.0.0/bin/llvm-symbolizer
By the way, some people may have installed llvm but not linked some binaries to path. The sure-fire way to add all llvm binaries to path is:
PATH="$PATH:$(brew --prefix)/opt/llvm/bin"
$(brew --prefix)/opt/llvm is a symbolic link to the most recent installed version of llvm, and bin is obviously the binaries therein.
I'm starting to learn Haskell and I found out that ghc can compile using LLVM with the -fllvm flag. Whenever I use the flag, I get the error message:
<no location info>: error:
Warning: Couldn't figure out LLVM version!
Make sure you have installed LLVM 3.7
ghc: could not execute: opt
However, I have opt in my /usr/local/Cellar/llvm/3.9.0/ folder. I'm on a Mac OS X and I've installed the full LLVM with brew install llvm but error persists. Is this a genuine version problem where I have to unistall LLVM and reinstall its 3.7 version? Or is ghc having trouble finding opt and there is some kind of search path I can modify to fix the problem? Thanks for the help and have a great day.
The GHC documentation says that it's compatible with llvm-2.8+, but as you've discovered, it actually requires llvm-3.7.
The simplest way to get it is:
brew install llvm#3.7
This installs llvm binaries in your path with a -3.7 suffix, like clang-3.7. GHC will need the unadorned names, which are in a subdirectory:
export PATH=/usr/local/opt/llvm#3.7/lib/llvm-3.7/bin:$PATH
To get support I am installing fink on my MacBook Pro. After execute bootstrap script I am getting following error log
Checking package... looks good (fink-0.35.1).
Checking system... i386-apple-darwin12.4.0
This system is supported and tested.
Distribution: 10.8
Architecture: x86_64
Checking cc... not found.
ERROR: There is no C compiler on your system. Make sure that the Developer
Tools are installed.
I didn't find gcc in /usr/bin/ directory.
After reading here, I am guessing x-code provide default support for gcc compiler.
any one have idea what I should to get support of fink or if have any other way to get support of apt-get.
First, you need to install Xcode and its command line tools to get the gcc compiler
Make sure that you have working version of gcc in your /usr/bin directory
Create a symbolic link cc from installed gcc in /usr/bin
I am attempting to build GCC-4.7.0 on a MacBook Pro running OS X 10.7.4. However, I am continuing to experience the same error:
configure: error: Building GCC requires GMP 4.2+, MPFR 2.3.1+ and MPC 0.8.0+.
This error occurred after running the following line:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/
To get rid of this error I have tried the following actions:
Using homebrew I downloaded gmp-5.0.4, mpc-0.21, and mpfr-3.1.0. At this point I attempting to point to where gmp, mpc, and mpfr are located with the following command:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/ --with-mpfr=/usr/local/Cellar/ --with-mpc=/usr/local/Cellar/
However, this caused the same error. So, I tried pointing gcc to various locations around the Cellar directory:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/gmp/ --with-mpfr=/usr/local/Cellar/mpfr --with-mpc=/usr/local/Cellar/mpc/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/gmp/5.0.4/ --with-mpfr=/usr/local/Cellar/mpfr/3.1.0/ --with-mpc=/usr/local/Cellar/mpc/0.21/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/gmp/5.0.4/include/ --with-mpfr=/usr/local/Cellar/mpfr/3.1.0/include/ --with-mpc=/usr/local/Cellar/mpc/0.21/share/
In the end these all produced the same error. I then downloaded the versions of gmp, mpc, and mpfr linked from the gcc error message (found here: ftp://gcc.gnu.org/pub/gcc/infrastructure/). After building these from the source and running all the same configurations I am left with the same problem. The configurations I have tried with this installation are:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/ --with-mpfr=/usr/local/ --with-mpc=/usr/local/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/include/ --with-mpfr=/usr/local/include/ --with-mpc=/usr/local/include/
Then I read somewhere that there could be a problem if I didn't explicitly set the configuration to run in 64-bit mode. So, I tried all of these configurations again with the added setting of 'CC=gcc -m64'. But this didn't change anything. If anyone has any ideas I would be greatly appreciative.
If you don't know how to build and properly direct GCC's configure to the libraries you can put them in the source tree of GCC itself:
/some/dir/source/gcc/[libstdc++|libgomp|gcc|libiberty|....]
/some/dir/source/gcc/gmp/[configure|...]
/some/dir/source/gcc/mpfr/[configure|...]
/some/dir/source/gcc/mpc/[configure|...]
So without the version number appended. Then just run GCC configure without any arguments related to GMP/MPC/MPFR.
I've faced the same issue and it was easily solved by installing the corresponding development packages: gmp-devel, mpfr-devel and libmpc-devel
Yigal
EasyBuild (a tool to make building software easier) can be of help here. It comes with a small easyconfig file that specifies which GCC version to build, and which features to enable (see for example https://github.com/hpcugent/easybuild/blob/master/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb).
Once you've downloaded EasyBuild and configured it, you can just run
$EBHOME/easybuild.sh myGCC.eb
with EBHOME set to the location where you unpacked EasyBuild, and myGCC.eb a copy of the example GCC easyconfig, which you modified to your needs.
This command will download the GCC source tarball for you and build/install it, after doing the same to any dependencies, for example GMP, MPFR and MPC, saving you a lot of headaches.
For more information on EasyBuild, see https://github.com/hpcugent/easybuild/wiki .
I have a Kubuntu 11.10 system with Eclipse-CDT Indigo. gcc-4.6 was installed along with Eclipse. I have since installed gcc-4.4 and gcc-4.2 via Ubuntu packages.
I can switch the /usr/bin/gcc symlink to 4.4 or 4.6 and Eclipse builds my code either way. However when I set the symlink to use gcc-4.2 I get the following error (and many more):
In file included from /usr/include/c++/4.2/cstring:52,
from /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h:47,
from /usr/include/c++/4.2/iosfwd:45,
from /usr/include/c++/4.2/ios:43,
from /usr/include/c++/4.2/ostream:45,
from /usr/include/c++/4.2/iostream:45,
from ../ProjStructure.h:4,
from ../Scanner.h:3,
from ../Scanner.cpp:1:
/usr/include/string.h:29: error: ‘__BEGIN_DECLS’ does not name a type
So it appears that the string.h I have in /usr/include expects __BEGIN_DECLS to be defined by one of the compiler specific includes.
/usr/include/string.h comes from the libc6-dev package, which does not seem to have compiler specific versions. I expected the package system to handle this and install all the right versions of things.
I've read the GNU documents on multiple versions of GCC, but they don't say anything about include files/directories.
What am I doing wrong here?
From which Ubuntu is your gcc-4.2 package?
It is probably from an older Ubuntu release. New Ubuntu releases have changed some header and library directories, which break older compilers.